WASHINGTON—The U.S. Senate ignored appeals by the Trump administration and passed a resolution on Thursday to withdraw U.S. support for the Saudi-led coalition at war in Yemen, delivering a bipartisan setback for the president’s Middle East policy.

The measure, which passed in a 56-41 vote, pits a Senate upset by the October killing of journalist Jamal Khashoggi by Saudi agents against the Trump administration, which views Saudi Arabia as a vital strategic ally. Seven Republicans joined with all 49 members of the Democratic caucus to support the resolution. Three Republican senators were absent.

The resolution, sponsored by Sens. Bernie Sanders (I., Vt.) and
Mike Lee
(R., Utah), would withdraw U.S. military support for the Saudi-led coalition fighting Iran-allied Houthi militants in a conflict that has left tens of thousands dead and pushed millions to the brink of starvation. Among other elements, it would bar U.S. refueling of Saudi planes and scale back the U.S. presence in the region.

While setting up a clash between the Senate and Trump administration, the resolution is unlikely to affect U.S. military policy in the region. House Republican leaders on Wednesday stopped an effort that would have forced a vote on a similar Yemen resolution on the floor.

How did the CIA conclude that journalist Jamal Khashoggi was killed on the orders of Saudi Crown Prince Mohammed bin Salman? WSJ’s Warren P. Strobel has an exclusive look at the secretive evidence behind the assessment. Photo: Reuters

“It’s important to send a message,” Mr. Sanders told reporters before the vote, adding that it could come up next year. “My very strong expectation is that in January, with Democratic control over the House, it will succeed.”

After the Senate approved the resolution, it also unanimously passed a resolution with broad bipartisan sponsorship that condemned the killing of Mr. Khashoggi and directly connected Saudi Crown
Prince Mohammed
bin Salman to the journalist’s death.

“It’s a strong statement of our condemnation of what has happened. To me, that’s important even if it doesn’t affect policy,” said
Sen. Bob Corker
(R., Tenn.).

The Saudi government has repeatedly said the crown prince had no knowledge of the operation.

The Wall Street Journal reported earlier this month that the Central Intelligence Agency determined in a highly classified assessment that Prince Mohammed sent at least 11 messages to his closest adviser, who oversaw the team that killed Mr. Khashoggi, in the hours before and after the journalist’s death.

Senior administration officials urged senators to vote against the Sanders-Lee resolution, arguing that withdrawing U.S. support would only harm the international effort to secure an end to the conflict and hinder efforts to contain Iran.

A Yemeni man sits in front of a destroyed building allegedly targeted by a Saudi-led airstrike, in San'a, Yemen, earlier this month.
Photo:
Yahya Arhab/EPA-EFE/REX/Shutterstock

Martin Griffiths,
the U.N. special envoy on Yemen, secured agreement on Thursday from both sides for a peaceful handover of control of the Hodeidah port from Houthi fighters to U.N. forces, a deal designed to avert a risky military fight for the country’s main gateway for humanitarian aid.

The agreement marked a rare moment of diplomatic success in the four-year-old conflict.

Mr. Griffiths is hoping to use the peace talks in Sweden as a launching pad for more substantive talks to resolve the war in Yemen, which the U.N. says is home to the worst humanitarian crisis in the world.

“The progress on the peace negotiations is not coincidental to this vote,” said
Sen. Chris Murphy
(D., Conn.). “The United States has said through the Senate that our support for the Saudi-led coalition is no longer open-ended. We expect our partners to be partners in peace.”

In addition to the Sanders-Lee resolution, the Senate is also reviewing a separate bill introduced last week by
Sen. Bob Menendez
(D., N.J.) and Sen. Todd Young (R., Ind.) that would suspend weapons sales to Saudi Arabia, sanction people who block humanitarian access in Yemen or aid Houthi rebels there, as well as sanction those responsible for Mr. Khashoggi’s death.

Also on Thursday, Rhode Island Sen. Jack Reed, the top Democrat on the Armed Services Committee, announced that the Department of Defense had discovered it had undercharged the Saudi-led coalition $331 million for fuel and aerial refueling services from 2015 to 2018, and planned to bill Saudi Arabia and the United Arab Emirates.

“While the accounting error is being corrected, the larger issue remains that the Trump Administration and international community must capitalize on the progress that has been made during the Yemen peace talks in Sweden,” Mr. Reed said.